From bb6836f31aafbbf6552d434a3f74a6fcd05ce662 Mon Sep 17 00:00:00 2001 From: ubyndr Date: Mon, 13 May 2024 14:43:16 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20INCATool?= =?UTF-8?q?s/pandasaurus=5Fcxg@bcad34d3a71de88c44d3f2a43819fef823ef8cce=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .buildinfo | 2 +- _modules/index.html | 2 +- .../pandasaurus_cxg/anndata_analyzer.html | 2 +- .../pandasaurus_cxg/anndata_enricher.html | 12 +- .../pandasaurus_cxg/enrichment_analysis.html | 2 +- .../graph_generator/graph_generator.html | 2 +- .../graph_generator_utils.html | 2 +- .../pandasaurus_cxg/utils/anndata_loader.html | 2 +- .../pandasaurus_cxg/utils/exceptions.html | 2 +- _static/basic.css | 2 +- _static/doctools.js | 2 +- _static/language_data.js | 4 +- _static/searchtools.js | 165 +++++++++++------- genindex.html | 2 +- index.html | 2 +- introduction.html | 2 +- pandasaurus_cxg/anndata_analyzer.html | 2 +- pandasaurus_cxg/anndata_enricher.html | 2 +- pandasaurus_cxg/enrichment_analysis.html | 2 +- .../graph_generator/graph_generator.html | 2 +- .../graph_generator_utils.html | 2 +- pandasaurus_cxg/graph_generator/index.html | 2 +- pandasaurus_cxg/index.html | 2 +- pandasaurus_cxg/utils/anndata_loader.html | 2 +- pandasaurus_cxg/utils/exception.html | 2 +- pandasaurus_cxg/utils/index.html | 2 +- py-modindex.html | 2 +- search.html | 2 +- searchindex.js | 2 +- 29 files changed, 141 insertions(+), 92 deletions(-) diff --git a/.buildinfo b/.buildinfo index c2d345b..47fa255 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 2b0adff3c8bf010f7feabb9f9c1e7ac1 +config: c4511841f97a030af4792e6187835bb8 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 88af1ab..13f64d3 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -13,7 +13,7 @@ - + diff --git a/_modules/pandasaurus_cxg/anndata_analyzer.html b/_modules/pandasaurus_cxg/anndata_analyzer.html index 4fe08db..5d9cb2b 100644 --- a/_modules/pandasaurus_cxg/anndata_analyzer.html +++ b/_modules/pandasaurus_cxg/anndata_analyzer.html @@ -13,7 +13,7 @@ - + diff --git a/_modules/pandasaurus_cxg/anndata_enricher.html b/_modules/pandasaurus_cxg/anndata_enricher.html index 5c544bf..8c8d7d6 100644 --- a/_modules/pandasaurus_cxg/anndata_enricher.html +++ b/_modules/pandasaurus_cxg/anndata_enricher.html @@ -13,7 +13,7 @@ - + @@ -122,10 +122,14 @@

Source code for pandasaurus_cxg.anndata_enricher

# TODO Do we need to keep whole anndata? Would it be enough to keep the obs only? self.anndata = anndata self.seed_dict = dict( - self.anndata.obs.drop_duplicates(subset=[cell_type_field, "cell_type"]).dropna()[ - [cell_type_field, "cell_type"] - ].values + self.anndata.obs.drop_duplicates(subset=[cell_type_field, "cell_type"]) + .dropna()[[cell_type_field, "cell_type"]] + .values ) + # "unknown" patch + if "unknown" in self.seed_dict: + del self.seed_dict["unknown"] + self.seed_dict["CL:0000000"] = "cell" self.enricher = Query(list(self.seed_dict.keys())) try: unique_context = self.anndata.obs[ diff --git a/_modules/pandasaurus_cxg/enrichment_analysis.html b/_modules/pandasaurus_cxg/enrichment_analysis.html index 8d8f934..248d8ef 100644 --- a/_modules/pandasaurus_cxg/enrichment_analysis.html +++ b/_modules/pandasaurus_cxg/enrichment_analysis.html @@ -13,7 +13,7 @@ - + diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html index aecb34b..6d972b9 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html @@ -13,7 +13,7 @@ - + diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html index f46a1b9..5edb733 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html @@ -13,7 +13,7 @@ - + diff --git a/_modules/pandasaurus_cxg/utils/anndata_loader.html b/_modules/pandasaurus_cxg/utils/anndata_loader.html index ddf23a8..d12e460 100644 --- a/_modules/pandasaurus_cxg/utils/anndata_loader.html +++ b/_modules/pandasaurus_cxg/utils/anndata_loader.html @@ -13,7 +13,7 @@ - + diff --git a/_modules/pandasaurus_cxg/utils/exceptions.html b/_modules/pandasaurus_cxg/utils/exceptions.html index cf80a17..270a0a8 100644 --- a/_modules/pandasaurus_cxg/utils/exceptions.html +++ b/_modules/pandasaurus_cxg/utils/exceptions.html @@ -13,7 +13,7 @@ - + diff --git a/_static/basic.css b/_static/basic.css index 30fee9d..f316efc 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/doctools.js b/_static/doctools.js index d06a71d..4d67807 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -4,7 +4,7 @@ * * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/language_data.js b/_static/language_data.js index 250f566..367b8ed 100644 --- a/_static/language_data.js +++ b/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -13,7 +13,7 @@ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/_static/searchtools.js b/_static/searchtools.js index 7918c3f..92da3f8 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +137,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +176,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -239,16 +268,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,16 +304,32 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - results.push([ + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -308,46 +344,47 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +398,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -466,14 +508,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +542,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -549,8 +594,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/genindex.html b/genindex.html index f7c0f6f..94be9a7 100644 --- a/genindex.html +++ b/genindex.html @@ -13,7 +13,7 @@ - + diff --git a/index.html b/index.html index a47511e..a7606bf 100644 --- a/index.html +++ b/index.html @@ -14,7 +14,7 @@ - + diff --git a/introduction.html b/introduction.html index 2d96130..c33f44a 100644 --- a/introduction.html +++ b/introduction.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/anndata_analyzer.html b/pandasaurus_cxg/anndata_analyzer.html index 35e514e..6575634 100644 --- a/pandasaurus_cxg/anndata_analyzer.html +++ b/pandasaurus_cxg/anndata_analyzer.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/anndata_enricher.html b/pandasaurus_cxg/anndata_enricher.html index e204ed5..a260a9a 100644 --- a/pandasaurus_cxg/anndata_enricher.html +++ b/pandasaurus_cxg/anndata_enricher.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/enrichment_analysis.html b/pandasaurus_cxg/enrichment_analysis.html index cf060be..4905d1a 100644 --- a/pandasaurus_cxg/enrichment_analysis.html +++ b/pandasaurus_cxg/enrichment_analysis.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/graph_generator/graph_generator.html b/pandasaurus_cxg/graph_generator/graph_generator.html index 867698a..29f6e29 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/pandasaurus_cxg/graph_generator/graph_generator.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/graph_generator/graph_generator_utils.html b/pandasaurus_cxg/graph_generator/graph_generator_utils.html index 1826a94..0c80ebf 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator_utils.html +++ b/pandasaurus_cxg/graph_generator/graph_generator_utils.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/graph_generator/index.html b/pandasaurus_cxg/graph_generator/index.html index f3c4d98..a4ec5ac 100644 --- a/pandasaurus_cxg/graph_generator/index.html +++ b/pandasaurus_cxg/graph_generator/index.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/index.html b/pandasaurus_cxg/index.html index 52bf02c..7e630dd 100644 --- a/pandasaurus_cxg/index.html +++ b/pandasaurus_cxg/index.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/utils/anndata_loader.html b/pandasaurus_cxg/utils/anndata_loader.html index 4825796..262701a 100644 --- a/pandasaurus_cxg/utils/anndata_loader.html +++ b/pandasaurus_cxg/utils/anndata_loader.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/utils/exception.html b/pandasaurus_cxg/utils/exception.html index 66e9244..b5f6376 100644 --- a/pandasaurus_cxg/utils/exception.html +++ b/pandasaurus_cxg/utils/exception.html @@ -14,7 +14,7 @@ - + diff --git a/pandasaurus_cxg/utils/index.html b/pandasaurus_cxg/utils/index.html index 0de42cf..565cb99 100644 --- a/pandasaurus_cxg/utils/index.html +++ b/pandasaurus_cxg/utils/index.html @@ -14,7 +14,7 @@ - + diff --git a/py-modindex.html b/py-modindex.html index d8a50fc..4d17abd 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -13,7 +13,7 @@ - + diff --git a/search.html b/search.html index bdc7154..ff96102 100644 --- a/search.html +++ b/search.html @@ -14,7 +14,7 @@ - + diff --git a/searchindex.js b/searchindex.js index ef7b7e8..89dfb02 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["index", "introduction", "pandasaurus_cxg/anndata_analyzer", "pandasaurus_cxg/anndata_enricher", "pandasaurus_cxg/enrichment_analysis", "pandasaurus_cxg/graph_generator/graph_generator", "pandasaurus_cxg/graph_generator/graph_generator_utils", "pandasaurus_cxg/graph_generator/index", "pandasaurus_cxg/index", "pandasaurus_cxg/utils/anndata_loader", "pandasaurus_cxg/utils/exception", "pandasaurus_cxg/utils/index"], "filenames": ["index.rst", "introduction.rst", "pandasaurus_cxg/anndata_analyzer.rst", "pandasaurus_cxg/anndata_enricher.rst", "pandasaurus_cxg/enrichment_analysis.rst", 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